Brexit poses a big threat to pharmaceutical research and manufacturing in the UK, the industry has said, potentially driving up manufacturing costs and deterring future investment.

AstraZeneca and other companies have frozen all manufacturing investments. Britain’s second-biggest drugmaker decided to halt further investments at its Macclesfield site in the summer of 2017. Its chairman, Leif Johansson, has said the UK needs to make sure it “does not become an isolated island in the middle of the Atlantic Ocean”.

David Jefferys, a senior executive at the European arm of the Japanese company Eisai, which makes treatments for Alzheimer’s disease, epilepsy and breast cancer, told the Guardian: “Nobody likes uncertainty. We are not making any new investments in the UK until there is clarity.”

Other major drugmakers, such as Novartis and the Viagra maker Pfizer, have announced plans to close UK manufacturing or packaging sites by 2020. Both decisions were made after the June 2016 referendum but the companies said they were not linked to Brexit.

Industry executives worry about their post-Brexit ability to bring highly skilled scientists to the UK, while researchers are concerned about being frozen out of EU-funded research collaborations. A no-deal Brexit would almost halve the UK’s funding from the EU’s Horizon 2020 programmme – a £70bn pot aimed at cutting-edge science – a report from the House of Lords said last week.

Britain has also lost the European Medicines Agency (EMA), which completed its move to Amsterdam last month, with the loss of 900 jobs.

Britain’s life sciences sector – pharmaceutical, medical technology and biotech companies and clinical research and regulatory organisations – employs 140,000 people directly but supports half a million jobs in total when the supply chain is included, according to a PricewaterhouseCoopers-commissioned review published in 2017. The sector contributed more than £30bn to the economy in 2015.

However, despite the scale of the UK drugs industry, two-thirds of the medicines used in the UK are imported from the EU and 90% come through Dover and Folkestone at present. Last summer the government told the pharma industry to increase its emergency supplies by an extra six weeks.

Companies have therefore ramped up their preparations for a no-deal Brexit, stockpiling medicines, duplicating drug testing, transferring licences and making plans to ship drugs to and from the EU on ferries leased by the government via six new port routes, from Immingham, Felixstowe, Poole, Plymouth, Portsmouth and Ramsgate.

The health secretary, Matt Hancock, has also chartered a plane to fly in medical isotopes for cancer treatment and other supplies with a short shelf life.

Mike Thompson, the Association of the British Pharmaceutical Industry’s chief executive, described Brexit as the biggest logistical challenge ever faced by the industry.